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I am new to editing roms and I just used CrystalTile2 to extract an arm9.bin from a rom, and used a hex editor to change some of the values. But I am not sure how to import/add the arm9.bin back into the roms files.

If you have not changed the size (changed say and sub command to a nop or add when it deals with lives sort of thing) then I quite like ndsts fromhttp://www.no-intro.org/tools.htm

If you are just doing it for your internal use for now then you can unpack the whole ROM and rebuild with ndstool or one of its many alternatives. You can do it for a final build as well but the ending patch might be bigger if everything is moved thanks to the rebuild.

For CT2 on the file browser if you right click the file you should have some options for it. One does compression (be aware I have seen it falsely accuse things of being compressed before) and the other should do straight import.
Speaking of alternatives then crystaltile2 gained some competition which does better for certain things, stuff like tinke being a good start.

Thanks I figured out how to import my file within CT2, but I am having a problem now. I get this message:
- File is too small! Enter a new location(V): No data after the previous position ROM makes new is recommended.

I am trying to change the shiny encounter rate in HG/SS ROM and these are the steps I've followed in a thread on another forum:
- Decompress arm9.bin
- Go to offset 0070080* and change the value 08 into FF
- Now I am trying to import this arm9.bin back into original ROM file

It is saying it wants you to unpack the whole ROM, swap out the file and rebuild, similar to the ndstool thing above. That or put a location somewhere else in the ROM for it to grab it from (don't know why it does not do it itself as it would be easy for a program to do but oh well. Alternatively the newly compressed file might be smaller than it was before but again it should have handled it better than that.